Project Summary Influenza virus causes significant morbidity and mortality worldwide annually. The virus has a broad tropism for epithelial cells in the respiratory tract. To clear the infection the immune system must confront these diverse cells which can be harboring different levels of virus or virus antigen:MHC, have differential expression of inhibitory ligands, and reside in different anatomical locations. To determine the long-term fate of virus infected cells we developed a novel virus capable of permanent labeling of infected cells in reporter mice. By inserting Cre recombinase into the virus genome, infection of mice expressing a Cre-inducible fluorophore permanently labels the cells and allows for long-term tracking and study of infected cells. Using this tool we made the surprising discovery that not all previously infected cells are killed by the lytic virus replication or the adaptive immune response. We hypothesize that CD8 T cells kill or pardon infected epithelial cells depending on cell type, the state of virus replication within the cell, and virus-induced expression of inhibitory ligands. We further hypothesize that surviving cells are critical mediators of pulmonary recovery. Because we can visualize cells throughout the clearance phase of infection we can exploit this system to study the epithelial cells that are killed by CD8 T cells and the mechanisms that permit infection. The goals of this proposal are to: 1) Determine the mechanisms of infected cell evasion from CD8 T cell-mediated killing 2) Define the roles of surviving cells in pulmonary repair and recovery 3) Map the infected cells that are eliminated by CD8 T cells and 4) Elucidate the mechanisms that protect and permit infection of new cells in the face of antiviral immune responses. Importantly, the indelible labeling system employed during these studies can be extended beyond IAV, to any virus that is amenable to foreign gene insertions. Results from this proposal will uncover fundamental mechanisms in antiviral immunity, cellular resistance and survival, and pulmonary recovery.